I have recently switched my project tables to InnoDB (thinking the relations would be a nice thing to have). I\'m using a PHP script to index about 500 products at a time. <
I had a similar problem and it seems InnoDB has by default innodb_flush_log_at_trx_commit enabled which flushes every insert/update query on your hdd log file. The writing speed of your hard disk is a bottleneck for this process.
So try to modify your mysql config file
`innodb_flush_log_at_trx_commit = 0`
Restart mysql service.
I experienced about x100 speedup on inserts.